Schema for UCSC liftOver mm10 - UCSC liftOver alignments to mm10
  Database: mm39    Primary Table: liftOverMm10    Row Count: 910   Data last updated: 2023-03-07
Format description: Summary info about a chain of alignments
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 608smallint(5) unsigned range Indexing field to speed chromosome range queries.
score 2498double range score of chain
tName chr1varchar(255) values Target sequence name
tSize 195154279int(10) unsigned range Target sequence size
tStart 3057785int(10) unsigned range Alignment start position in target
tEnd 3057813int(10) unsigned range Alignment end position in target
qName chrXvarchar(255) values Query sequence name
qSize 171031299int(10) unsigned range Query sequence size
qStrand -char(1) values Query strand
qStart 105415357int(10) unsigned range Alignment start position in query
qEnd 105415385int(10) unsigned range Alignment end position in query
id 21759545int(10) unsigned range chain id

Sample Rows

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

UCSC liftOver mm10 (liftOverMm10) Track Description


This track shows the 'lift over' calculated alignments from the mm10/mouse to the mm39/mouse genome assembly, used by the UCSC liftOver tool.

Display Conventions and Configuration

The alignments are shown as "chains" of alignable regions. The display is similar to the other chain tracks, see our chain display documentation for more information.

Data access

UCSC liftOver chain files for mm10 to mm39 can be obtained from a dedicated directory on our download server mm10/liftOver directory. Specifically, the mm39ToMm10.over.chain.gz file.

The table can also be explored interactively with the Table Browser or the Data Integrator.


The lift over chain file is constructed with the doSameSpeciesLiftOver processing using the blat genome alignment program.